Topics

1

General Questions and Answers / VNL nanotube grower question

« on: September 18, 2009, 16:57 »

Hi all,

In Nanotube Grower, carbon nanotube period length is shown dependent on the indices and the C-C bond length. Which formula is used in this tool to calculate the period from the bond length? Could you please give the formula and a reference?

Thanks a lot,

Serhan

2

General Questions and Answers / Transmission spectrum of CNT

« on: August 24, 2009, 19:22 »

Hi all,

When I calculate the transmission spectrum of an ideal CNT for different bias voltages in ATK , I see that the transmission spectrum changes by the bias voltage a lot. Is it normal, if it is normal what is the reason of the change of transmission spectrum bu bias voltage? Any references would be appreciated.

Cheers,
Serhan

3

General Questions and Answers / Density of states

« on: July 19, 2009, 21:10 »

I'd like to ask how can we calculate the density of states and plot it for carbon nanotubes in ATK? We have *.nc files of the simulations of various metallic CNTs (two-probe simulations). How can we extract DOS from these *.nc files?

Cheers,
Serhan

4

General Questions and Answers / Choice of basis

« on: April 26, 2009, 07:02 »

Hi,

What is the criterion for the choice of basis set type? Element type or geometry or so? To be spesific, can we use SZ sets for graphene calculations?

Cheers,
Serhan

5

General Questions and Answers / "Killed signal 9" error

« on: April 23, 2009, 04:59 »

Hi all,

I'm trying to simulate a (6,6) perfect nanotube. My py file is attached. I have 4 reps in electrodes and 10 reps in central region. But, ATK (or MPI) gives the error:

Code

# ----------------------------------------------------------------
# Electrodes Calculation
# ----------------------------------------------------------------
# sc  0 : Fermi Energy =    0.00000 Ry
rank 0 in job 2  node01_40687   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9 

Is there  a way to overcome this problem?

Cheers,
Serhan

6

General Questions and Answers / St9_badalloc error

« on: April 20, 2009, 18:38 »

Hi,

I'm trying to calculate scf of a (6,6) carbon nanotube but ATK gives the error:

Code

master@node01:~$ mpiexec -n 12 /home/master/atk-2008.10.0/bin/atk /home/master/6/6_6_nanotube_script.py > /home/master/6.dat &
[1] 10244
master@node01:~$ Traceback (most recent call last):
  File "<string>", line 916, in ?
ATKError: St9bad_alloc

I searched google, some say that this is caused from insufficient memory. My simulation includes 480 carbon atoms. I'm using LDA with 150 Ry cut-off. Each machine uses 2GB RAM with 64-bit Ubuntu and I'm using 6 PCs in parallel.

Cheers,
Serhan

7

Future Releases / Usage of graphics card for future ATK technology

« on: April 17, 2009, 20:52 »

Hi,

I've a suggestion for the speed up of ATK for the future releases. We've used an electromagnetic software and the provider offered an acceleration option using the specially designed cards using GPU (Graphical Processing Unit) for FDTD calculations. The link is as follows for the accelerator cards: http://www.remcom.com/xf7/xstream . I do not know what happens exactly inside the ATK motor (I know very complex thing occur ), but I thought ATK may use an accelerator solution.

Cheers,
Serhan

8

General Questions and Answers / How to optimize a nanotube

« on: April 12, 2009, 21:53 »

Hi all,

There are optimization options in Nanolanguage scripter as steepest descent and quasi-Newton. Suppose we have a nanotube geometry generated in Nanotube grower. How can we optimize this nanotube structure by NL code or scripter?

Cheers,
Serhan

9

General Questions and Answers / A multi-walled CNT structure creation as two-probe

« on: April 12, 2009, 20:03 »

Dear all,

I'm trying to set up a structure as follows:

The scattering region: A double-walled CNT structure composed of (5,5) and (12,12) CNTs. The electrodes: From the left hand side, I want to set up the electrode as (5,5), and at the right hand side set up the electrode as (12,12). In other words, (5,5) CNT will continue at left as left electrode while (12,12) will continue at the right to form right probe. 

By such a configuration, I can calculate the transport (if any) between shells  . I prepared the scattering region as attached by using some information posted previously on this forum.  But I could not probe the scattering region as I defined above. Could you please help? 

Cheers,
Serhan

10

General Questions and Answers / Energy-band diagram of 2D graphene

« on: March 28, 2009, 23:02 »

Hi,

I followed the graphene tutorial. I get the E-k diagram shown with Fig. 6 in the tutorial. However, I could not reproduce the 2-D dispersion relation (Fig. 7). How can I get Fig. 7 from Fig. 6? Or will I get the E-k values from the command prompt and then plot it in MATLAB etc?

Cheers
Serhan

11

General Questions and Answers / Kinetic energy per unit lenght

« on: March 23, 2009, 10:55 »

Is it possible to calculate the kinetic energy per unit lenght in ATK? Or indirectly, is it possible to calculate Fermi velocity?

Cheers,
Serhan

12

General Questions and Answers / How to change positions of atoms by script

« on: January 24, 2009, 08:48 »

Hello all,

I'm trying to re-position the atoms of any structure (any periodic or molecule configuration) in nanolanguage. In other words, I'm trying to modify coordinates of atoms according to some rule, for example, "increase the x position by 2 Angstrom while keeping other positions unchanged" or "double the x and z coordinate while y coordinate is unchanged", in fact this corresponds the modifying the origin in Atomic Manipulator.

Since atom coordinates are given as a list of lists, I have to loop over each element of list of lists. I studied the script below to modify the coordinates of (5,5) nanotube such that "double the x and y coordinate while z coordinate is unchanged". But I could not complete the script. Could you help please?

Code

coordinates = [[  1.23252581e+01,   8.93048313e+00,   0.00000000e+00],
               [  1.16769137e+01,   1.09258818e+01,   1.23148812e+00],
               [  9.97952627e+00,   1.21591059e+01,  -2.22044605e-16],
               [  7.88143998e+00,   1.21591059e+01,   1.23148812e+00],
               [  6.18405251e+00,   1.09258818e+01,  -4.44089210e-16],
               [  5.53570819e+00,   8.93048313e+00,   1.23148812e+00],
               [  6.18405251e+00,   6.93508448e+00,  -8.88178420e-16],
               [  7.88143998e+00,   5.70186030e+00,   1.23148812e+00],
               [  9.97952627e+00,   5.70186030e+00,  -8.88178420e-16],
               [  1.16769137e+01,   6.93508448e+00,   1.23148812e+00],
               [  1.20317643e+01,   1.03112625e+01,  -5.55111512e-17],
               [  1.06278706e+01,   1.18704445e+01,   1.23148812e+00],
               [  8.57563252e+00,   1.23066611e+01,  -2.22044605e-16],
               [  6.65893531e+00,   1.14532926e+01,   1.23148812e+00],
               [  5.60989217e+00,   9.63629652e+00,   0.00000000e+00],
               [  5.82920190e+00,   7.54970376e+00,   1.23148812e+00],
               [  7.23309566e+00,   5.99052179e+00,  -8.88178420e-16],
               [  9.28533373e+00,   5.55430512e+00,   1.23148812e+00],
               [  1.12020309e+01,   6.40767370e+00,  -8.88178420e-16],
               [  1.22510741e+01,   8.22466973e+00,   1.23148812e+00]]

for index1, item1 in enumerate(coordinates):
  for index2, item2 in enumerate(item1):
    if index2==0:
      item_new[index2]=2*item1[index2]
    elif index2==1:
      item_new[index2]=2*item1[index2]
    elif index2==2:
      item_new[index2]=item1[index2]

Regards

Serhan

13

Installation and License Questions / Best and fast configuration for running ATK

« on: January 19, 2009, 09:35 »

Hi all,

I tried ATK on a 64-bit linux machine but I'll re-install my system. For the best ATK performance, which version would you recommend? 32-bit or 64-bit? I'll use mpi to parallelize the ATK.

Cheers
Serhan

14

General Questions and Answers / start and end time of ATK job

« on: January 13, 2009, 10:26 »

Hello,

How can I print the start and end time of an ATK simulation? When I start ATK inside VNL it prints the start and end time but when I start ATK alone from command prompt, it does not print time?

Regards

Serhan

15

Installation and License Questions / lmgrd error

« on: January 6, 2009, 18:24 »

Hi all,

I tried to install ATK 2008.10 64 bit version on a machine running 64 bit Ubuntu. But when I unzipped the ATK installer from the QW site and tried to run the command

Code

./lmgrd -c demo4.lic

the commad line gives the error:

Code

No such file or directory.

Terminal is at /home/user1/atk10/bin directory and when I give the command ls, it shows the file lmgrd. I also checked that lmgrd has an executable attribute. What is wrong here?

Regards,
Serhan